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Yorodumi- EMDB-17187: 48-nm repeat of the native axonemal doublet microtubule from bovi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17187 | |||||||||
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Title | 48-nm repeat of the native axonemal doublet microtubule from bovine sperm | |||||||||
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Sample |
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Keywords | microtubule / cilia / sperm / axoneme / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / regulation of calcineurin-NFAT signaling cascade / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility ...outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / regulation of calcineurin-NFAT signaling cascade / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / cilium-dependent cell motility / positive regulation of feeding behavior / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / cerebrospinal fluid circulation / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of cilium beat frequency involved in ciliary motility / sperm principal piece / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / MAP kinase tyrosine/serine/threonine phosphatase activity / COPI-mediated anterograde transport / RHO GTPases Activate Formins / cilium movement involved in cell motility / 9+2 motile cilium / regulation of store-operated calcium entry / cilium movement / Transferases; Transferring phosphorus-containing groups / calcium ion sensor activity / acrosomal membrane / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / sperm DNA condensation / flagellated sperm motility / cilium organization / axonemal microtubule / Aggrephagy / gamma-tubulin ring complex / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / negative regulation of TOR signaling / nucleotide-activated protein kinase complex / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / GTP biosynthetic process / microtubule organizing center / Neutrophil degranulation / nucleoside diphosphate kinase activity / ciliary base / myosin phosphatase activity / intercellular bridge / beta-tubulin binding / regulation of neuron projection development / AMP binding / regulation of cell division / single fertilization / axoneme / spermatid development / cerebral cortex cell migration / mitotic cytokinesis / alpha-tubulin binding / cilium assembly / cellular response to UV-C / sperm flagellum / phosphatase binding / cellular response to glucose starvation / dephosphorylation / sperm midpiece / Hsp70 protein binding / 3'-5' exonuclease activity / centriole / mitotic spindle organization / acrosomal vesicle / ciliary basal body / meiotic cell cycle / protein tyrosine phosphatase activity / cell projection / G protein-coupled receptor binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / protein localization Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Leung MR / Zeng J / Zhang R / Zeev-Ben-Mordehai T | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Cell / Year: 2023 Title: Structural specializations of the sperm tail. Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai / Abstract: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17187.map.gz | 277.9 MB | EMDB map data format | |
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Header (meta data) | emd-17187-v30.xml emd-17187.xml | 103.5 KB 103.5 KB | Display Display | EMDB header |
Images | emd_17187.png | 94 KB | ||
Filedesc metadata | emd-17187.cif.gz | 22.7 KB | ||
Others | emd_17187_additional_1.map.gz emd_17187_half_map_1.map.gz emd_17187_half_map_2.map.gz | 179 MB 1010.4 MB 1009.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17187 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17187 | HTTPS FTP |
-Related structure data
Related structure data | 8otzMC 8ou0C 8snbC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17187.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_17187_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17187_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17187_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 48-nm repeat of the native axonemal doublet microtubule from bovi...
+Supramolecule #1: 48-nm repeat of the native axonemal doublet microtubule from bovi...
+Macromolecule #1: Cilia- and flagella-associated protein 95
+Macromolecule #2: Sperm acrosome associated 9
+Macromolecule #3: Testis specific serine kinase 6
+Macromolecule #4: EF-hand domain-containing protein
+Macromolecule #5: ATP6V1F neighbor
+Macromolecule #6: Outer dense fiber of sperm tails 3 like 1
+Macromolecule #7: Outer dense fiber of sperm tails 3
+Macromolecule #8: Tubulin alpha-3 chain
+Macromolecule #9: Tubulin beta-4B chain
+Macromolecule #10: Protein Flattop
+Macromolecule #11: Cilia- and flagella-associated protein 53
+Macromolecule #12: Nucleoside diphosphate kinase 7
+Macromolecule #13: EF-hand domain-containing family member C2
+Macromolecule #14: Family with sequence similarity 166 member A
+Macromolecule #15: Protein FAM166C
+Macromolecule #16: Outer dense fiber of sperm tails 3B
+Macromolecule #17: Spermatid-specific manchette-related protein 1
+Macromolecule #18: Enkurin
+Macromolecule #19: Coiled-coil domain-containing protein 105
+Macromolecule #20: Protein phosphatase 1 regulatory subunit 32
+Macromolecule #21: RIB43A-like with coiled-coils protein 2
+Macromolecule #22: Cilia- and flagella-associated protein 107
+Macromolecule #23: Piercer of microtubule wall 1 protein
+Macromolecule #24: Piercer of microtubule wall 2 protein
+Macromolecule #25: Stabilizer of axonemal microtubules 1
+Macromolecule #26: Stabilizer of axonemal microtubules 3
+Macromolecule #27: Meiosis-specific nuclear structural protein 1
+Macromolecule #28: Tektin-3
+Macromolecule #29: Tektin-5
+Macromolecule #30: Sperm-associated antigen 8
+Macromolecule #31: Spermatogenesis-associated protein 48
+Macromolecule #32: Tektin-1
+Macromolecule #33: Tektin-2
+Macromolecule #34: Uncharacterized protein C1orf100 homolog
+Macromolecule #35: TEPP protein
+Macromolecule #36: Uncharacterized protein MGC137036
+Macromolecule #37: Testis expressed 33
+Macromolecule #38: Testis-expressed sequence 37 protein
+Macromolecule #39: Testis-expressed protein 43
+Macromolecule #40: Testis expressed 49
+Macromolecule #41: Theg spermatid protein like
+Macromolecule #42: EF-hand domain-containing family member B
+Macromolecule #43: Tektin bundle interacting protein 1
+Macromolecule #44: Tektin-4
+Macromolecule #45: Chromosome 7 open reading frame 31
+Macromolecule #46: Cilia- and flagella- associated protein 210
+Macromolecule #47: EF-hand domain-containing protein 1
+Macromolecule #48: Uncharacterized protein C10orf82 homolog
+Macromolecule #49: Cilia- and flagella-associated protein 144
+Macromolecule #50: Chromosome 20 C5orf49 homolog
+Macromolecule #51: Chromosome 19 C17orf98 homolog
+Macromolecule #52: Chromosome 13 C20orf85 homolog
+Macromolecule #53: Cilia- and flagella-associated protein 68
+Macromolecule #54: Cilia and flagella associated protein 77
+Macromolecule #55: UPF0602 protein C4orf47 homolog
+Macromolecule #56: Cilia- and flagella-associated protein 20
+Macromolecule #57: Parkin coregulated gene protein
+Macromolecule #58: CFAP97 domain containing 1
+Macromolecule #59: Cilia- and flagella-associated protein 45
+Macromolecule #60: Cilia- and flagella-associated protein 52
+Macromolecule #61: Cilia- and flagella-associated protein 141
+Macromolecule #62: Cilia- and flagella-associated protein 161
+Macromolecule #63: Dual specificity phosphatase 21
+Macromolecule #64: Uncharacterized protein C4orf45 homolog
+Macromolecule #65: Cilia- and flagella-associated protein 276
+Macromolecule #66: EF-hand calcium-binding domain-containing protein 3
+Macromolecule #67: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #68: MAGNESIUM ION
+Macromolecule #69: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 532665 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 34083 |